Genital warts can be external, on the outside areas of your reproductive organs, or they can appear internally where you cannot see them. Internal warts can develop on the cervix, urethra, anus or inside the vagina, according to the New Zealand Dermatological Society's information resource Dermnet NZ. All genital warts are caused by strains of HPV, or human papilloma virus. Removing internal warts does not eradicate the virus from your body, but simply eliminates the protrusions.

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Topical Solutions

Topical solutions in the form of creams, acids or other liquid chemicals can be used in some cases to treat internal warts. Due to the hard-to-reach locations in which the growths are found, most of these solutions must be applied by a medical care provider rather than self-administration. One cream-based treatment called Imiquimod may be self-applied, and is more effective in treating female internal warts that those in males. Other topical treatments to remove internal genital warts include trichloroacetic acid--TCA--a very caustic liquid that burns away warts in the anal or vaginal region, according to the American Academy of Family Physicians. TCA is usually recommended when you have smaller warts that are moist and affect only a small area of your genitals, rather than large clusters.

Cryosurgery

Cryosurgery is a common treatment for genital warts of both external and internal varieties. Cryosurgery involves exposing the abnormal tissue to liquid nitrogen. The liquid nitrogen freezes the wart and the surrounding skin to remove the growth. Cryosurgery is done as an outpatient procedure with a local anesthetic, and is considered one of the safer options for pregnant women with internal warts.

Surgical Excision

Internal warts that cannot be removed through acid treatments or crysosurgery can be removed through a more invasive surgical process. The American Academy of Family Physicians explains that surgical excision probes deeper into the dermal level, can be more painful than less invasive means and may cause scarring. Removing warts surgically carries a small risk of infection.

Laser Removal

Dermnet reports that a widespread outbreak of warts, especially those in areas that are harder to access, such as the urethra or cervix, may be removed through laser procedures. Laser treatment is advised for people with HIV or others with a compromised immune system.